A global RNA analysis of Neisseria gonorrhoeae in vitro and during human infection

Thesis (Ph.D.)--Boston UniversityThe mucosal disease, gonorrhea, caused by the Gram-negative pathogen Neisseria gonorrhoeae, is estimated to have at least 700,000 cases annually in the United States and 62 million cases worldwide. A strict human pathogen, N. gonorrhoeae infects several mucosal sites throughout the body making proper gene regulation crucial. The goal of these studies was to define the global transcriptional response of N. gonorrhoeae during infection by analyzing its transcriptome during in vitro growth, during incubation with human epithelial cells, and during in vivo mucosal infection of the human female genital tract. Using RNA sequencing, we identified several new small RNA transcripts expressed in vitro that have the potential to regulate target mRNAs. Our studies were aided by the development of a novel computer program, Rockhopper, designed specifically for analysis of prokaryotic transcriptomes. Secondary methods were used to corroborate a strong correlation between Rockhopper analysis and N. gonorrhoeae transcriptional start sites, operon structures and gene expression levels. We also utilized Rockhopper to analyze the gonococcal transcriptome expressed during incubation with a human endocervical cell line. During such incubation, N. gonorrhoeae was demonstrated to regulate a large number of stress response and respiratory genes. Corresponding analysis of host cells during incubation with N. gonorrhoeae revealed increased expression of host pathways involved in innate immunity, adaptive immunity, cancer and apoptosis. Finally, analysis of gonococcal RNA from four vaginal lavage samples of female patients exposed to partners infected with N. gonorrhoeae was performed. This analysis demonstrated a similar profile of gonococcal stress response genes compared to incubation with epithelial cells. In addition, several novel sRNAs expressed by the gonococcus only during in vivo infection were also identified. Analysis of the same vaginal lavage samples demonstrated that a number of human genes involved in immune pathways and cancer are expressed during mucosal gonococcal infection. These studies are the first to analyze gene regulation in N. gonorrhoeae globally during infection and greatly expand our knowledge of how the host and pathogen respond to infection. Furthermore, they have the potential to aid in the development of novel antibacterial therapeutics or new vaccine targets for this disease

Public Libraries and the Internet 2006

Examines the capability of public libraries to provide and sustain public access Internet services and resources that meet community needs, including serving as the first choice for content, resources, services, and technology infrastructure

The role of voltage-gated potassium channels in the regulation of mouse uterine contractility

<p>Abstract</p> <p>Background</p> <p>Uterine smooth muscle cells exhibit ionic currents that appear to be important in the control of uterine contractility, but how these currents might produce the changes in contractile activity seen in pregnant myometrium has not been established. There are conflicting reports concerning the role of voltage-gated potassium (Kv) channels and large-conductance, calcium-activated potassium (BK) channels in the regulation of uterine contractility. In this study we provide molecular and functional evidence for a role for Kv channels in the regulation of spontaneous contractile activity in mouse myometrium, and also demonstrate a change in Kv channel regulation of contractility in pregnant mouse myometrium.</p> <p>Methods</p> <p>Functional assays which evaluated the effects of channel blockers and various contractile agonists were accomplished by quantifying contractility of isolated uterine smooth muscle obtained from nonpregnant mice as well as mice at various stages of pregnancy. Expression of Kv channel proteins in isolated uterine smooth muscle was evaluated by Western blots.</p> <p>Results</p> <p>The Kv channel blocker 4-aminopyridine (4-AP) caused contractions in nonpregnant mouse myometrium (EC50 = 54 micromolar, maximal effect at 300 micromolar) but this effect disappeared in pregnant mice; similarly, the Kv4.2/Kv4.3 blocker phrixotoxin-2 caused contractions in nonpregnant, but not pregnant, myometrium. Contractile responses to 4-AP were not dependent upon nerves, as neither tetrodotoxin nor storage of tissues at room temperature significantly altered these responses, nor were responses dependent upon the presence of the endometrium. Spontaneous contractions and contractions in response to 4-AP did not appear to be mediated by BK, as the BK channel-selective blockers iberiotoxin, verruculogen, or tetraethylammonium failed to affect either spontaneous contractions or 4-AP-elicited responses. A number of different Kv channel alpha subunit proteins were found in isolated myometrium from both nonpregnant and term-pregnant mice, and one of these proteins – Kv4.3 – was found to disappear in term-pregnant tissues.</p> <p>Conclusion</p> <p>These findings suggest a role for Kv channels in the regulation of uterine contractility, and that changes in the expression and/or function of specific Kv channels may account for the functional changes seen in pregnant myometrium.</p

HD 209621: Abundances of neutron-capture elements

High resolution spectra obtained from the Subaru Telescope High Dispersion Spectrograph have been used to update the stellar atmospheric parameters and metallicity of the star HD 209621. We have derived a metallicity of [Fe/H] = -1.93 for this star, and have found a large enhancement of carbon and of heavy elements, with respect to iron. Updates on the elemental abundances of four s-process elements (Y, Ce, Pr, Nd) along with the first estimates of abundances for a number of other heavy elements (Sr, Zr, Ba, La, Sm, Eu, Er, Pb) are reported. The stellar atmospheric parameters, the effective temperature, Teff, and the surface gravity, log g (4500 K, 2.0), are determined from LTE analysis using model atmospheres. Estimated [Ba/Eu] = +0.35, places the star in the group of CEMP-(r+s) stars; however, the s-elements abundance pattern seen in HD 209621 is characteristic of CH stars; notably, the 2nd-peak s-process elements are more enhanced than the first peak s-process elements. HD 209621 is also found to show a large enhancement of the 3rd-peak s-process element lead (Pb) with [Pb/Fe] = +1.88. The relative contributions of the two neutron-capture processes, r- and s- to the observed abundances are examined using a parametric model based analysis, that hints that the neutron-capture elements in HD 209621 primarily originate in s-process.Comment: 16 pages,8 figures. Accepted for publication in MNRA

Effective permeability of an immiscible fluid in porous media determined from its geometric state

Based on the phenomenological extension of Darcy's law, two-fluid flow is dependent on a relative permeability function of saturation only that is process/path dependent with an underlying dependency on pore structure. For applications, fuel cells to underground $CO_2$ storage, it is imperative to determine the effective phase permeability relationships where the traditional approach is based on the inverse modelling of time-consuming experiments. The underlying reason is that the fundamental upscaling step from pore to Darcy scale, which links the pore structure of the porous medium to the continuum hydraulic conductivities, is not solved. Herein, we develop an Artificial Neural Network (ANN) that relies on fundamental geometrical relationships to determine the mechanical energy dissipation during creeping immiscible two-fluid flow. The developed ANN is based on a prescribed set of state variables based on physical insights that predicts the effective permeability of 4,500 unseen pore-scale geometrical states with $R^2 = 0.98$.Comment: 6 Pages, 2 Figures, and Supporting Materia

Phenotypic responses to interspecies competition and commensalism in a naturally derived microbial co-culture

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL- 58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL- 48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold

Sickle cell trait and risk of cognitive impairment in African-Americans: The REGARDS cohort

Background: Sickle cell anemia may be associated with cognitive dysfunction, and some complications of sickle cell anemia might affect those with sickle cell trait (SCT), so we hypothesized that SCT is a risk factor for cognitive impairment. Methods: The Reasons for Geographic and Racial Differences in Stroke (REGARDS) study enrolled a national cohort of 30,239 white and black Americans from 2003 to 7, who are followed every 6 months. Baseline and annual global cognitive function testing used the Six-Item Screener (SIS), a validated instrument (scores range 0-6; ≤ 4 indicates cognitive impairment). Participants with baseline cognitive impairment and whites were excluded. Logistic regression was used to calculate the association of SCT with incident cognitive impairment, adjusted for risk factors. Linear mixed models assessed multivariable-adjusted change in test scores on a biennially administered 3-test battery measuring learning, memory, and semantic and phonemic fluency. Findings: Among 7743 participants followed for a median of 7·1 years, 85 of 583 participants with SCT (14·6%) developed incident cognitive impairment compared to 902 of 7160 (12·6%) without SCT. In univariate analysis, the odds ratio (OR) of incident cognitive impairment was 1·18 (95% CI: 0·93, 1·51) for those with SCT vs. those without. Adjustment did not impact the OR. There was no difference in change on 3-test battery scores by SCT status (all p > 0·11). Interpretation: In this prospective cohort study of black Americans, SCT was not associated with incident cognitive impairment or decline in test scores of learning, memory and executive function. Funding: National Institutes of Health, American Society of Hematology

Relative permeability as a stationary process: energy fluctuations in immiscible displacement

Relative permeability is commonly used to model immiscible fluid flow through porous materials. In this work we derive the relative permeability relationship from conservation of energy, assuming that the system to be non-ergodic at large length scales and relying on averaging in both space and time to homogenize the behavior. Explicit criteria are obtained to define stationary conditions: (1) there can be no net change for extensive measures of the system state over the time averaging interval; (2) the net energy inputs into the system are zero, meaning that the net rate of work done on the system must balance with the heat removed; and (3) there is no net work performed due to the contribution of internal energy fluctuations. Results are then evaluated based on direct numerical simulation. Dynamic connectivity is observed during steady-state flow, which is quantitatively assessed based the Euler characteristic. We show that even during steady-state flow at low capillary number ($\mathsf{Ca}\sim1\times10^5$), typical flow processes will explore multiple connectivity states. The residence time for each connectivity state is captured based on the time-and-space average. The distribution for energy fluctuations is shown to be multi-modal and non-Gaussian when terms are considered independently. However, we demonstrate that their sum is zero. Given an appropriate choice of the thermodynamic driving force, we show that the conventional relative permeability relationship is sufficient to model the energy dissipation in systems with complex pore-scale dynamics that routinely alter the structure of fluid connected pathways